Showing : SingleCell • reset
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
6 months ago info ▴ 10
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Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
7 months ago xiaolong • 0
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527
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
11 months ago Silvio • 0
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
13 months ago Peter Hickey ▴ 750
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1
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1.1k
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'Seurat' package
singlecell seurat
updated 23 months ago by ★ 4.8k • written 23 months ago by ▴ 10
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1
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1.2k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 23 months ago by ▴ 750 • written 23 months ago by • 0
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2
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981
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
24 months ago paria.alipour • 0
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2
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1.3k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.1 years ago Assa Yeroslaviz ★ 1.5k
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4
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1.2k
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Single-cell differential expression analysis with multiple samples
SingleCell
2.1 years ago iaradsouza1 • 0
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8
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1.7k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 17 months ago by • 0 • written 2.1 years ago by • 0
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
2.1 years ago Laurent Gatto 1.6k
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3
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2.0k
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Knee and Inflection of DropletUtils
SingleCell
updated 2.1 years ago by ★ 4.8k • written 2.2 years ago by • 0
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1
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4.4k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
1
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1.2k
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.2 years ago by ★ 13k • written 2.2 years ago by ▴ 70
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950
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.2 years ago Jenny Drnevich ★ 2.0k
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3
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1.2k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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1
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923
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.4 years ago by ★ 2.0k
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3
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1.9k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 months ago by • 0 • written 2.4 years ago by • 0
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1
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981
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
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1.2k
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
2.5 years ago sudhir.thakurela • 0
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762
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Gene Id duplicated
SingleCell SingleCellData
updated 2.6 years ago by ★ 4.8k • written 2.6 years ago by • 0
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1.1k
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
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731
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weighting sample group
monocle SingleCell DifferentialExpression
2.6 years ago Sogand • 0
2
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2
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1.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.6 years ago k1m ▴ 20
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2
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1.6k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
2.6 years ago Guandong Shang ▴ 40
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4
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1.3k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.6 years ago Romina • 0
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1
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1.6k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.6 years ago by 68k • written 2.7 years ago by • 0
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1.8k
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by • 0
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2
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2.0k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
2.8 years ago fluentin44 • 0
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940
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.8 years ago Nik Tuzov ▴ 90
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.0 years ago zroger499 • 0
2
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1
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1.0k
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3.0 years ago by ▴ 90 • written 3.0 years ago by • 0
2
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1
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2.3k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
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1.1k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.3 years ago zroger499 • 0
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0
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1.2k
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.3 years ago Sebastian Lewandowski • 0
2
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2
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1.5k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.4 years ago by ★ 4.8k • written 3.4 years ago by ▴ 40
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
3.6 years ago lpinello • 0
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2
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1.5k
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
3.6 years ago Andrew Pattison • 0
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973
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Spike-In Cells for Normalization?
SpikeIn SingleCell
3.7 years ago mb1996 • 0
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981
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
3.7 years ago camp ▴ 10
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1.2k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.7 years ago lianov • 0
0
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1
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1.3k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
3
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2
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3.1k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.2 years ago camerond • 0
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1.3k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.3 years ago Steve Lianoglou ★ 13k
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2
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1.8k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.4 years ago jirkanov • 0
3
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1
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2.3k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
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1
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1.1k
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
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1.1k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.5 years ago hamza_karakurt ▴ 60
2
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6
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3.0k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
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6
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3.5k
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Awards • All
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Scholar to Gordon Smyth 52k
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